Let's draw a vertical pool in a diagram.
We set the Preferences: Horizontal layout of pools: Always false.
Now we draw a wide and short VERTICAL pool.
Then save and exit.
When we re-open the diagram there is a high and narrow pool, instead of a wide and short one.
It seems that the modeler says: "hey, horizontal is not allowed!", and exchanges height and width (with some problems for the pool content).
Note that the pools continues to be a vertical one (label at the top) as per our preferences.

Analogous behavior with the horizontal layout.
In this case Preferences are set to: Horizontal layout of pools: Always true.
Now we draw a horizontal pool and we make it high and narrow.
Save and exit the diagram, then open it again.
The modeler changes the aspect of the horizontal pool which becomes wide and short instead of high and narrow.

Bugzilla report opened.
I can't post the link to Bugzilla here because of a strange error: "You can only use links to eclipse.org sites while you have fewer than 5 messages."
The bug number is 453172, on bugs.eclipse.org/bugs/, product=BPMN2Modeler
Aldo